Many PocketPC's and other PDA's with an infared hookup can also be used as a programmable remote. As far as I know, the stock Sony Reader lacks this feature and is unable to do this.
However, you can build or purchase addon IR units to do this. Here is one device:
http://iguanaworks.net/product1.psp
We would need someone familiar with the reader, LINUX, and the software to determine if the device can work this way.
oops... missread the email -- you wanted a remote device to do page turns and not act as a tv or stereo remote control.....